[R-sig-ME] modeling question
Ben Bolker
bbolker at gmail.com
Thu Jan 26 20:17:43 CET 2017
On 17-01-26 02:11 PM, Joaquín Aldabe wrote:
> Thanks Ben, I sent all emails to the whole list. See below (in caps lock
> for differentiating from the other text). Regards, Joaquin
>
> 2017-01-26 15:59 GMT-03:00 Ben Bolker <bbolker at gmail.com
> <mailto:bbolker at gmail.com>>:
>
> On Thu, Jan 26, 2017 at 9:38 AM, Joaquín Aldabe
> <joaquin.aldabe at gmail.com <mailto:joaquin.aldabe at gmail.com>> wrote:
> > Dear Ben, it's me again
>
>
> (I don't mind if you cc: me, but this is really a question to the
> list. Probably better to frame it as "I sent this to the list and Ben
> Bolker said ...")
>
> > with this subject about invertebrate biomass and its
> > possible effect on shorebird density. I have a couple of extra doubts about
> > your recommendations:
>
>
> >
> > You suggested this:
> >
> > (1) The relationship between bird density and invert biomass, as well
> > as the intercept (i.e., expected bird density at invert_biomass=0, or
> > better invert_biomass=<some sensible reference quantity>).
> >
> > I tried a quantity considering the lowest value of the invertebrate biomass
> > variable, but the model did not converge. So I wonder if I should pick this
> > value or a different one?
>
> Hmm, is this with lme or lmer? Can you give more detail? If it's
> lmer, it's quite likely a false positive. I USED LME. I DON'T REALLY
> KNOW WHAT DO YOU EXACTLY MEAN WITH SENSIBLE REFERENCE QUANTITY. I
> THOUGHT IT WAS THE MINIMUM VALUE OF MY X VARIABLE (AS CERO IS NOT A
> POSSIBILITY).
>
The minimum value of your x variable is sensible. The mean or median
would also be sensible. It will change the interpretation of your
intercept parameter, and might improve convergence, but if the model
does converge then it won't change the overall fit of the model.
If you're using lme and re-locating your x variable (i.e. using
I(invert_biomass-ref_value)) doesn't help with convergence, then there
might be something else wrong. We need more information (what was the
error message? What are the general properties of your data?) and
preferably a reproducible example ...
> >
> > (2) The relationship might be changing over time?
> >
> > lme(Bird.density~Invertebrate biomass+sample_time,
> > random=~invert_biomass|Plot_identity, data=)
> >
> > How should I treat sample time? Is it a ordered categorical variable?
>
> Depends on a number of things. Your original message suggested
> that you sampled over the course of 30 days (maybe at different times
> in different plots?) If this is the case (e.g. you sampled plot 1 on
> days 1, 5, 9, ... and plot 2 on days 2, 6, 10 ...) then it is probably
> most sensible to treat time as a numeric variable (i.e., assume a
> linear trend over days) and possibly a random effect with days as a
> grouping variable (in which case you might have to switch from lme to
> lmer). If you have a small number of distinct sample days then a
> categorical variable makes sense. Whether you specify it as ordered or
> (default) unordered doesn't affect the overall fit of the model, just
> the particular contrasts that get tested with respect to the time
> variable.
>
>
> >
> > Thankyou very much.
> >
> > Joaquin
> >
> >
> > 2017-01-16 19:49 GMT-03:00 Ben Bolker <bbolker at gmail.com
> <mailto:bbolker at gmail.com>>:
> >>
> >>
> >> Center your biomass variable on this value: either create a
> >>
> >> mydata$invert_biomass_c <- mydata$invert_biomass-ref_value
> >>
> >> or include it directly in your formula:
> >>
> >> bird_dens ~ I(invert_biomass-ref_value), ...
> >>
> >> On 17-01-16 05:44 PM, Joaquín Aldabe wrote:
> >> > Thankyou very much Ben. Can you please suggest a way of fixing some
> >> > sensible reference quantity for Invertebrate biomass?
> >> > All the best,
> >> > Joaquín
> >> >
> >> > 2017-01-16 18:59 GMT-03:00 Ben Bolker <bbolker at gmail.com
> <mailto:bbolker at gmail.com>
> >> > <mailto:bbolker at gmail.com <mailto:bbolker at gmail.com>>>:
> >> >
> >> > That seems perfectly reasonable. There are a couple of
> things to
> >> > consider, although you may or may not find that your data
> supports
> >> > that much complexity.
> >> >
> >> > (1) The relationship between bird density and invert
> biomass, as
> >> > well
> >> > as the intercept (i.e., expected bird density at
> invert_biomass=0,
> >> > or
> >> > better invert_biomass=<some sensible reference quantity>)
> >> >
> >> > lme(Bird.density~Invertebrate biomass,
> >> > random=~invert_biomass|Plot_identity, data=)
> >> >
> >> >
> >> > (2) The relationship might be changing over time?
> >> >
> >> > lme(Bird.density~Invertebrate biomass+sample_time,
> >> > random=~invert_biomass|Plot_identity, data=)
> >> >
> >> > (3) In principle you could consider random effects of both
> time and
> >> > invert biomass, but that will almost certainly overwhelm
> your data.
> >> >
> >> > Don't forget to do the standard post-fitting checks: are your
> >> > residuals *approximately* equal-variance and (even more
> >> > approximately)
> >> > Normally distributed? Is the relationship between bird
> density and
> >> > invert biomass *approximately* linear? (See ?plot.lme)
> >> >
> >> >
> >> > On Mon, Jan 16, 2017 at 2:06 PM, Joaquín Aldabe
> >> > <joaquin.aldabe at gmail.com <mailto:joaquin.aldabe at gmail.com>
> <mailto:joaquin.aldabe at gmail.com <mailto:joaquin.aldabe at gmail.com>>>
> wrote:
> >> > > Dear all, I'm interested in modeling the effect of
> invertebrate
> >> > biomass on
> >> > > the density of a grassland shorebird (they eat
> invertebrates). For
> >> > this, I
> >> > > picked 8 plots and sampled invertebrates and birds 6
> times in each
> >> > plot for
> >> > > about 30 days. This is, I went to each plot and did repeated
> >> > measures of
> >> > > invertebrates biomass and shorebird density separated in
> time by
> >> > four or
> >> > > five days, as invertebrates biomass may change over time
> and it is
> >> > expected
> >> > > that birds density change accordingly.
> >> > >
> >> > > So, I'm trying to see a general pattern of the effect of
> changes
> >> > in biomass
> >> > > on the density of this shorebird species at a plot scale.
> Plot
> >> > identity is
> >> > > not important; I consider them as particular events of a
> random
> >> > process.
> >> > >
> >> > > Is this model correct:
> >> > >
> >> > > lme(Bird.density~Invertebrate biomass,
> random=~1|Plot_identity,
> >> > data=)
> >> > >
> >> > > Thank you very much,
> >> > >
> >> > > Joaquin.
> >> > >
> >> > >
> >> > > --
> >> > > *Joaquín Aldabe*
> >> > >
> >> > > *Grupo Biodiversidad, Ambiente y Sociedad*
> >> > > Centro Universitario de la Región Este, Universidad de la
> >> > República
> >> > > Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
> >> > >
> >> > > *Departamento de Conservación*
> >> > > Aves Uruguay
> >> > > BirdLife International
> >> > > Canelones 1164, Montevideo
> >> > >
> >> > > https://sites.google.com/site/joaquin.aldabe
> <https://sites.google.com/site/joaquin.aldabe>
> >> > <https://sites.google.com/site/joaquin.aldabe
> <https://sites.google.com/site/joaquin.aldabe>>
> >> > >
> <https://sites.google.com/site/perfilprofesionaljoaquinaldabe
> <https://sites.google.com/site/perfilprofesionaljoaquinaldabe>
> >> >
> <https://sites.google.com/site/perfilprofesionaljoaquinaldabe
> <https://sites.google.com/site/perfilprofesionaljoaquinaldabe>>>
> >> > >
> >> > > [[alternative HTML version deleted]]
> >> > >
> >> > > _______________________________________________
> >> > > R-sig-mixed-models at r-project.org
> <mailto:R-sig-mixed-models at r-project.org>
> >> > <mailto:R-sig-mixed-models at r-project.org
> <mailto:R-sig-mixed-models at r-project.org>> mailing list
> >> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
> >> > <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>>
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > *Joaquín Aldabe*
> >> >
> >> > /Grupo Biodiversidad, Ambiente y Sociedad/
> >> > Centro Universitario de la Región Este, Universidad de la República
> >> > Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
> >> >
> >> > /Departamento de Conservación/
> >> > Aves Uruguay
> >> > BirdLife International
> >> > Canelones 1164, Montevideo
> >> >
> >> > https://sites.google.com/site/joaquin.aldabe
> <https://sites.google.com/site/joaquin.aldabe>
> >> > <https://sites.google.com/site/perfilprofesionaljoaquinaldabe
> <https://sites.google.com/site/perfilprofesionaljoaquinaldabe>>
> >> >
> >> >
> >> >
> >
> >
> >
> >
> > --
> > Joaquín Aldabe
> >
> > Grupo Biodiversidad, Ambiente y Sociedad
> > Centro Universitario de la Región Este, Universidad de la República
> > Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
> >
> > Departamento de Conservación
> > Aves Uruguay
> > BirdLife International
> > Canelones 1164, Montevideo
> >
> > https://sites.google.com/site/joaquin.aldabe
> <https://sites.google.com/site/joaquin.aldabe>
> >
> >
> >
>
>
>
>
> --
> *Joaquín Aldabe*
>
> /Grupo Biodiversidad, Ambiente y Sociedad/
> Centro Universitario de la Región Este, Universidad de la República
> Ruta 15 (y Ruta 9), Km 28.500, Departamento de Rocha
>
> /Departamento de Conservación/
> Aves Uruguay
> BirdLife International
> Canelones 1164, Montevideo
>
> https://sites.google.com/site/joaquin.aldabe
> <https://sites.google.com/site/perfilprofesionaljoaquinaldabe>
>
>
>
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